Chairman Lord Justice Leveson has repeatedly declared he has no intention to gag the press, but there are concerns that his report will recommend huge changes to regulation that could see the end of the British media as we know it.

Editors expressed concern during their evidence at what the effect of the wide-ranging inquiry could be.

But it was Chris Blackhurst, the editor of the Independent, who went as far as branding the probe "deeply flawed".

Speaking at a debate at City University in London, he said the press was capable of creating reforms without a public inquiry, and newspapers had "held back" on coverage of the suicide of Wales football manager Gary Speed in November 2011 because of fears of the inquiry.

Mr Blackhurst said the Leveson Inquiry was "set up in a flawed way" as a political response to a "growing embarrassment", and voiced concerns that because it ran alongside criminal investigations, Lord Justice Leveson was limited in the evidence he could hear.

The chairman himself has suggested the second part of the inquiry – into specific allegations of wrongdoing at the News of the World – may not go ahead.

With the need to await the conclusion of police investigations and possible trials it could be "many months" before it can begin, he said, and suggested consideration should be given to its value bearing in mind the "enormous cost" to taxpayers.

Education Secretary Michael Gove – himself a former journalist – also hit out at the "chilling effect" of the inquiry on journalism.

His comments prompted Lord Justice Leveson to raise concerns with Downing Street, in turn sparking fears that the judge was trying to gag criticism of his inquiry.

Prompted to explain why he had stepped in, the chairman insisted he had no "hidden agenda" but was concerned the inquiry was being undermined.

Mr Gove repeated his concerns when he gave his evidence, saying inquiry recommendations are often "applied in a way that the cure is worse than the disease".

"Some of us believe that before the case for regulation is made, the case for liberty needs to be asserted as well," the Education Secretary added.

But he was met with an apparent slap down by the chairman who, when the minister raised concerns about restraints on the "precious liberty" of freedom of speech, told him: "I do not need to be told about the importance of freedom of speech, I really don't."

There were also questions asked over the difficulty of regulating web news publishers and bloggers.

Daily Mail online editor Martin Clarke said: "You can't slice and dice the internet up into different bits…Stephen Fry has four million followers on Twitter.

"He can reach more people in one hour than I can, so is he going to be regulated?"

Some witnesses were concerned by the lag between criticism and their opportunity to defend themselves,

Former culture secretary Jeremy Hunt asked to move his appearance forward in the wake of claims over the BSkyB bid but was turned down.

And while Charlotte Church's evidence about performing at Rupert Murdoch's wedding for favourable coverage rather than a £100,000 fee was taken as fact, it was months later that her former manager Jonathan Shalit wrote to Lord Justice Leveson to claim it was untrue.

Some critics felt the inquiry was allowed to extend too far.

As more allegations emerged over close ties between politicians and the press, eight Government ministers applied to be added to the list of core participants, allowing them to see documents and statements in advance.

But as questioning extended far and wide around the intricacies of relationships with so many key figures and the press, for some the inquiry became simply too wide.

Lord Justice Leveson himself spoke of his hope that his long-awaited report will not just "sit on the second shelf" in a journalism professor's study.

But for someone who, in the early days, summed up the main issue of the inquiry with the question: "Who guards the guardians?", Lord Justice Leveson will be more than aware of veteran reporter Jeremy Paxman's question.